Contacts of the strand formed by residues 45 - 51 (chain S) in PDB entry 3TDD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 45 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S ILE 5.3 1.0 + - - -
41S ARG* 3.2 5.5 - - - +
42S SER* 2.8 27.5 + - - +
43S ASN 3.8 0.2 - - - -
44S THR* 1.3 115.2 + - - +
46S ALA* 1.3 61.5 + - - +
146S ALA* 3.5 7.0 - - - +
184S GLY* 4.5 10.9 + - - -
185S ASN 5.0 1.6 + - - -
186S PRO* 4.1 23.9 - - + +
189S LEU* 3.6 19.7 - - + -
214S ILE* 3.5 33.7 - - + -
215S VAL 3.4 9.6 - - - +
216S GLY* 4.2 2.2 - - - -
217S LYS* 5.0 6.7 - - + -
218S ASP 5.6 0.4 - - - -
219S THR* 3.5 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40S LEU 3.4 6.7 - - - -
41S ARG* 3.8 9.0 - - + -
45S HIS* 1.3 76.3 - - - +
47S VAL* 1.3 64.1 + - - +
139S ILE* 3.6 29.6 - - + +
140S GLY 4.4 1.8 - - - +
146S ALA* 4.4 6.5 - - + -
147S HIS 3.8 12.8 - - - +
214S ILE* 3.5 4.7 - - - +
215S VAL* 3.0 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S GLY* 3.2 5.9 - - - -
40S LEU* 2.6 47.6 + - + +
46S ALA* 1.3 80.8 - - - +
48S LEU* 1.3 67.8 + - - +
49S VAL* 3.9 22.7 - - + -
139S ILE* 4.2 2.5 - - - +
189S LEU* 3.9 32.5 - - + +
190S ILE* 4.1 17.9 - - + -
212S ILE* 4.0 12.8 - - + -
213S ALA 3.4 11.0 - - - +
214S ILE* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S VAL 3.4 10.8 - - - +
39S GLY* 3.9 7.2 - - - -
47S VAL* 1.3 72.8 - - - +
49S VAL* 1.3 62.2 + - - +
67S ILE* 3.8 10.0 - - + +
75S GLY 4.3 0.2 - - - -
76S LEU* 3.5 38.6 - - - +
77S SER* 3.6 21.8 - - - +
137S LEU* 3.9 11.2 - - + +
139S ILE* 3.4 44.2 - - + -
212S ILE* 3.2 6.2 - - - +
213S ALA* 2.8 46.8 + - + +
221S PHE* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S THR* 3.4 1.3 + - - -
38S VAL* 2.5 47.2 + - + +
40S LEU* 4.8 2.2 - - + -
47S VAL* 3.9 15.5 - - + -
48S LEU* 1.3 75.6 - - - +
50S ALA* 1.3 61.2 + - - +
190S ILE 4.4 3.1 - - - +
193S GLY* 3.7 31.4 - - - +
194S VAL* 4.0 10.1 - - + +
197S ILE* 3.7 28.4 - - + +
210S LEU* 3.8 20.9 - - + -
211S SER 3.5 2.7 - - - -
212S ILE* 4.2 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37S THR* 2.9 27.4 - - - +
48S LEU 4.1 0.2 - - - -
49S VAL* 1.3 73.3 - - - +
51S LEU* 1.3 62.7 + - - +
52S LYS 3.5 2.1 + - - -
66S LYS* 3.9 25.1 - - + -
67S ILE* 4.3 14.4 - - + -
77S SER* 4.6 0.4 - - - -
197S ILE* 3.8 4.5 - - - -
210S LEU* 4.4 2.0 - - - +
211S SER* 2.8 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ASN* 3.1 45.3 - - + +
35S SER* 2.4 37.0 + - - +
36S VAL* 3.0 38.3 + - + +
50S ALA* 1.3 70.9 - - - +
52S LYS* 1.3 59.3 + - - +
53S ARG* 5.9 0.4 - - - -
66S LYS* 3.5 7.5 - - - -
168S ARG* 6.2 2.2 - - - +
197S ILE* 3.6 10.7 - - + +
200S SER 5.7 0.7 - - - +
201S LEU* 3.9 28.5 - - + -
204S GLU* 5.6 4.9 - - + +
207S LEU* 4.9 5.2 - - + -
210S LEU* 5.5 1.6 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il